Go Back   SEQanswers > Applications Forums > Clinical Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
big variant database: do you want to share? tdm Bioinformatics 0 10-31-2012 11:10 AM
mean position of the variant within the variant supporting reads alg Bioinformatics 0 07-10-2012 10:52 AM
Genomic Sequence Database vs Chromosomal sequence database ? Arupsss Bioinformatics 2 06-20-2012 10:22 AM
What do you do with your database? quantrix Bioinformatics 4 02-25-2011 05:39 PM

Thread Tools
Old 01-29-2014, 03:26 PM   #1
Senior Member
Location: chicago

Join Date: Jul 2012
Posts: 354
Default variant database

Is there a publically avaliable database of clinically known variants? What we do is upload a list of genes and get the known pathogenic variants in this gene. Currently we do this manually every 3 moths with HGMD, but that is getting too dificult and I would like to automate that process. Thank you.
cmccabe is offline   Reply With Quote
Old 01-30-2014, 04:05 AM   #2
Senior Member
Location: Budapest

Join Date: Mar 2010
Posts: 329

The dbSNP contains information about pathogenic variations.
There is a tool Genes2FANS which do the same task (upload genes and see connections with known disease).
This tool is based on OMIM.
TiborNagy is offline   Reply With Quote
Old 01-31-2014, 05:47 AM   #3
Junior Member
Location: US

Join Date: Jul 2012
Posts: 2

Well, HGMD Professional is still the best source of data on germline mutations. Similar type of information could be found in OMIM and ClinVar as well, however HGMD is manually curated and just comparing numbers it has about 150k mutations while OMIM has 22k and ClinVar 67k. It could take a lot of effort to regularly extract information in bulk from online version of HGMD as you do with gene panels, but that's what download version is for. It comes as simple relational database (MySQL) and querying it is very easy.
Factor is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:24 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO